6CWY

Crystal structure of SUMO E1 in complex with an allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.462 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular mechanism of a covalent allosteric inhibitor of SUMO E1 activating enzyme.

Lv, Z.Yuan, L.Atkison, J.H.Williams, K.M.Vega, R.Sessions, E.H.Divlianska, D.B.Davies, C.Chen, Y.Olsen, S.K.

(2018) Nat Commun 9: 5145-5145

  • DOI: 10.1038/s41467-018-07015-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • E1 enzymes activate ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) in the first step of Ub/Ubl conjugation cascades and represent potential targets for therapeutic intervention in cancer and other life-threatening diseases. Here, we report the cr ...

    E1 enzymes activate ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) in the first step of Ub/Ubl conjugation cascades and represent potential targets for therapeutic intervention in cancer and other life-threatening diseases. Here, we report the crystal structure of the E1 enzyme for the Ubl SUMO in complex with a recently discovered and highly specific covalent allosteric inhibitor (COH000). The structure reveals that COH000 targets a cryptic pocket distinct from the active site that is completely buried in all previous SUMO E1 structures and that COH000 binding to SUMO E1 is accompanied by a network of structural changes that altogether lock the enzyme in a previously unobserved inactive conformation. These structural changes include disassembly of the active site and a 180° rotation of the catalytic cysteine-containing SCCH domain, relative to conformational snapshots of SUMO E1 poised to catalyze adenylation. Altogether, our study provides a molecular basis for the inhibitory mechanism of COH000 and its SUMO E1 specificity, and also establishes a framework for potential development of molecules targeting E1 enzymes for other Ubls at a cryptic allosteric site.


    Organizational Affiliation

    Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, 91010, CA, USA.,Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, 29425, SC, USA.,Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, 29425, SC, USA. olsensk@musc.edu.,Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, 32827, FL, USA.,Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, 91010, CA, USA. ychen@coh.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUMO-activating enzyme subunit 1
C
346Homo sapiensMutation(s): 0 
Gene Names: SAE1 (AOS1, SUA1, UBLE1A)
Find proteins for Q9UBE0 (Homo sapiens)
Go to Gene View: SAE1
Go to UniProtKB:  Q9UBE0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SUMO-activating enzyme subunit 2
D
660Homo sapiensMutation(s): 0 
Gene Names: UBA2 (SAE2, UBLE1B)
EC: 2.3.2.-
Find proteins for Q9UBT2 (Homo sapiens)
Go to Gene View: UBA2
Go to UniProtKB:  Q9UBT2
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FHJ
Query on FHJ

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D
dimethyl (1S,2S,3R,4R)-1-[(1S)-2-(4-methylphenyl)-1-(phenylamino)ethyl]-7-oxabicyclo[2.2.1]hept-5-ene-2,3-dicarboxylate
C25 H27 N O5
AOCBOTNEIQNHIY-OAKYZLIPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.462 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.055α = 90.00
b = 116.046β = 90.00
c = 174.143γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115568-02

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2020-01-01
    Type: Author supporting evidence